Alpha Centauri is an obvious choice, but I'd also recommend looking at Galactic Civilizations 2. AC is available on gog.com, sadly sans expansion while GalCiv2 is on Steam and Impulse (whatever it's called these days).

If you end up getting AC I fully expect a report on how you ended up blowing Planet to smithereens just to shut that nutter, Sister Miriam, up.

And if it's GalCiv2 I want a story of how you got in a massive war with the dictatorial space apes.

Edit: neither are free. AC is 6$ I think and GalCiv2 Complete is 15€. I don't know what that translates to in $.